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- PDB-4pin: Ergothioneine-biosynthetic methyltransferase EgtD in complex with... -

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Basic information

Entry
Database: PDB / ID: 4pin
TitleErgothioneine-biosynthetic methyltransferase EgtD in complex with N,N-dimethylhistidine
ComponentsHistidine-specific methyltransferase EgtD
KeywordsTRANSFERASE / methyltransferase / ergothioneine / histidine betaine
Function / homology
Function and homology information


L-histidine Nalpha-methyltransferase / L-histidine N(alpha)-methyltransferase activity / ergothioneine biosynthesis from histidine via gamma-glutamyl-hercynylcysteine sulfoxide / protein methyltransferase activity / methylation
Similarity search - Function
Methyltransferase EgtD-like / Histidine-specific methyltransferase, SAM-dependent / Histidine N-alpha-methyltransferase, Actinobacteria-type / Histidine N-alpha-methyltransferase / : / Histidine-specific methyltransferase, SAM-dependent / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N,N-dimethyl-L-histidine / PHOSPHATE ION / Histidine N-alpha-methyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVit, A. / Seebeck, F.P. / Blankenfeldt, W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Foundation147005 Switzerland
Citation
Journal: Chembiochem / Year: 2015
Title: Ergothioneine Biosynthetic Methyltransferase EgtD Reveals the Structural Basis of Aromatic Amino Acid Betaine Biosynthesis.
Authors: Vit, A. / Misson, L. / Blankenfeldt, W. / Seebeck, F.P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization and preliminary X-ray analysis of the ergothioneine-biosynthetic methyltransferase EgtD.
Authors: Vit, A. / Misson, L. / Blankenfeldt, W. / Seebeck, F.P.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine-specific methyltransferase EgtD
B: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4079
Polymers70,5652
Non-polymers8417
Water12,250680
1
A: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7515
Polymers35,2831
Non-polymers4684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine-specific methyltransferase EgtD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6564
Polymers35,2831
Non-polymers3733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.988, 74.757, 137.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histidine-specific methyltransferase EgtD / Histidine-alpha-N-methyltransferase


Mass: 35282.695 Da / Num. of mol.: 2 / Mutation: T2A, A29T, P30Q, A75S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 607 / Gene: egtD, MSMEG_6247, MSMEI_6086 / Plasmid: pET19m / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0R5M8, L-histidine Nalpha-methyltransferase
#2: Chemical ChemComp-AVI / N,N-dimethyl-L-histidine


Mass: 183.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N3O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 1.6 M sodium phosphate, 0.4 M dipotassium phosphate, 0.1 M sodium phosphate citrate, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→49.778 Å / Num. all: 59396 / Num. obs: 59396 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 23.07 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.105 / Rsym value: 0.094 / Net I/av σ(I): 7.024 / Net I/σ(I): 10.9 / Num. measured all: 294015
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-24.90.6741.24241885750.3350.6742.3100
2-2.1250.4591.74031181010.2280.4593.2100
2.12-2.2750.3022.63810776420.150.3024.8100
2.27-2.4550.233.43552571120.1140.235.9100
2.45-2.6950.155.13285565900.0750.158.6100
2.69-350.17.52973159790.050.112.4100
3-3.4750.06410.82630253000.0320.06420.1100
3.47-4.254.90.04914.22221045130.0250.04926.9100
4.25-6.014.90.03817.21722735410.0190.03829.399.8
6.01-49.7784.60.03112.6932920430.0170.03129.799.2

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
XDSdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4PIM

4pim


Resolution: 1.9→49.778 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 2991 5.05 %
Rwork0.1978 56252 -
obs0.2 59243 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.05 Å2 / Biso mean: 31.5467 Å2 / Biso min: 14.82 Å2
Refinement stepCycle: final / Resolution: 1.9→49.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4921 0 77 680 5678
Biso mean--26.35 35.26 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035070
X-RAY DIFFRACTIONf_angle_d0.796896
X-RAY DIFFRACTIONf_chiral_restr0.03787
X-RAY DIFFRACTIONf_plane_restr0.003904
X-RAY DIFFRACTIONf_dihedral_angle_d12.9731816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93120.44891330.416726592792100
1.9312-1.96450.39581390.324626582797100
1.9645-2.00020.31761430.262626452788100
2.0002-2.03860.28421340.234926442778100
2.0386-2.08030.2581350.219426572792100
2.0803-2.12550.24221490.216526392788100
2.1255-2.17490.2411460.222526432789100
2.1749-2.22930.33781240.25872633275799
2.2293-2.28960.41391460.32112622276899
2.2896-2.3570.23851530.200126612814100
2.357-2.4330.25681470.189826422789100
2.433-2.520.22581380.18526842822100
2.52-2.62090.23681630.189426492812100
2.6209-2.74020.25151420.192126812823100
2.7402-2.88460.2511460.196626992845100
2.8846-3.06530.22841460.192226802826100
3.0653-3.3020.22851330.185926922825100
3.302-3.63420.21071330.165827132846100
3.6342-4.15980.20991500.159127372887100
4.1598-5.240.16261360.143827542890100
5.24-49.79490.20821550.18842860301599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.68920.2792-0.38670.73030.0720.26060.0791-0.1775-0.05330.0695-0.0459-0.0368-0.00630.0329-0.02210.206-0.0138-0.03670.26010.07760.232712.076916.677920.5332
21.5804-0.50350.13961.25070.03892.11540.152-0.0483-0.1349-0.0279-0.0604-0.15470.1830.0496-0.11740.2747-0.0384-0.02570.269-0.04360.226722.701728.670319.8666
30.88030.2908-0.20431.1833-0.38220.82240.0515-0.146-0.04080.01710.06370.1490.0054-0.1493-0.11430.14260.005-0.01790.20260.05830.15584.312116.520416.907
43.1831.5852-0.40630.9354-0.39150.3776-0.09910.1777-0.2328-0.05880.10130.03850.0684-0.02120.02710.3392-0.0403-0.02520.26630.04630.240634.9961-6.26221.0382
50.770.00310.0920.8006-0.49630.7772-0.0907-0.0281-0.0542-0.13260.1665-0.05770.1155-0.0655-0.07050.2065-0.0231-0.06670.24440.12470.320424.1936-5.932816.5132
63.35751.1086-1.00431.072-0.36341.12720.0157-0.14940.39310.03280.04360.2687-0.2563-0.0916-0.06230.28170.0628-0.05140.30930.06240.242944.91463.069524.399
71.5846-0.31750.25581.0044-0.28312.1012-0.0179-0.1227-0.08970.038-0.0687-0.08560.0953-0.00540.11810.2706-0.0215-0.01950.24220.08880.212945.04373.41499.8351
81.07330.09080.17460.5612-0.18141.1135-0.0002-0.1022-0.1639-0.10070.06940.10940.2141-0.0586-0.06230.2516-0.0051-0.03470.1920.09460.246430.6239-12.190419.2186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 77 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 145 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 321 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 26 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 27 through 57 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 102 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 103 through 145 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 321 )B0

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